Fix bugs and example docs unearthed by building reference

R/AAAClassDefinitions.R

@@ -78,16 +78,14 @@ SsimLibrary <- setClass("SsimLibrary", contains = "SsimObject",
 #' Scenario. 0 indicates this is not a result Scenario
 #' @slot folderId integer. The folder in which the Scenario exists. If the Scenario
 #' exists at the root of the project, then this value is NULL.
-#' @slot breakpoints list of Breakpoint objects (optional)
 #' @name Scenario-class
 #' @rdname Scenario-class
 #' @export Scenario
 Scenario <- setClass("Scenario", contains = "SsimObject", 
                      representation(projectId = "numeric", 
                                     scenarioId = "numeric", 
                                     parentId = "numeric", 
-                                    folderId = "numeric", 
-                                    breakpoints = "list"))
+                                    folderId = "numeric"))
 
 #' SyncroSim Project class
 #'

R/addPackage.R

@@ -25,7 +25,8 @@ NULL
 #' @examples
 #' \donttest{
 #' # Install "stsim" and "stsimecodep" SyncroSim packages
-#' installPackage("stsim")
+#' installPackage(packages = c("stsim", "stsim"),
+#'                versions = c("4.0.0", "4.0.1"))
 #' installPackage("stsimecodep")
 #' 
 #' # Specify file path and name of new SsimLibrary

R/chart.R

@@ -36,7 +36,7 @@ setMethod(
 
       charts <- subset(charts, ChartId == chart)
 
-      # If no folders retrieved, then ID does not yet exist
+      # If no charts retrieved, then ID does not yet exist
       if (nrow(charts) == 0){
         stop(paste0("The project does not contain the given chart ID ", 
                     chart,
@@ -46,7 +46,7 @@ setMethod(
 
       if (create == TRUE) {
         stop(paste0("Cannot create a new chart from a chart ID. Please provide",
-                    " a name for the new folder and the ID will be assigned",
+                    " a name for the new chart and the ID will be assigned",
                     " automatically."))
       }
 
@@ -123,14 +123,16 @@ setMethod(
 #' 
 #' # Set the SyncroSim Session, SsimLibrary, Project, and Scenario
 #' mySession <- session()
-#' myLibrary <- ssimLibrary(name = myLibraryName, session = mySession) 
+#' myLibrary <- ssimLibrary(name = myLibraryName, 
+#'                          session = mySession,
+#'                          packages = "stsim") 
 #' myProject <- project(myLibrary, project = "My Project")
 #' myScenario <- scenario(myProject, scenario = "My Scenario")
 #' 
 #' # Create a new chart
 #' myChart <- chart(myProject, chart = "New Chart")
 #' }
-#' @name folder
+#' @name chart
 #' @export
 chart <- function(ssimObject = NULL, chart = NULL, create = FALSE, summary = FALSE){
 
@@ -140,7 +142,7 @@ chart <- function(ssimObject = NULL, chart = NULL, create = FALSE, summary = FAL
 
   # if ssimObject is a library throw an error
   if (is.element(class(ssimObject), c("SsimLibrary"))) {
-    stop("Cannot create a folder at the Library-level.")
+    stop("Cannot create a chart at the Library-level.")
   }
 
   # Return chart data if no chart argument is specified

R/chartId.R

@@ -15,12 +15,13 @@ NULL
 #' @examples 
 #' \donttest{
 #' # Set the file path and name of the new SsimLibrary
-#' myLibraryName <- file.path(tempdir(),"testlib")
+#' myLibraryName <- file.path(tempdir(), "testlib")
 #' 
 #' # Set the SyncroSim Session, SsimLibrary, and Project
 #' mySession <- session()
 #' myLibrary <- ssimLibrary(name = myLibraryName, 
 #'                          session = mySession, 
+#'                          packages = "stsim",
 #'                          overwrite = TRUE) 
 #' myProject <- project(myLibrary, project = "Definitions")
 #' 

R/command.R

@@ -42,8 +42,8 @@ NULL
 #' 
 #' # Specify the command line arguments for creating a new stsim SsimLibrary
 #' args <- list(create = NULL, library = NULL, 
-#'         name = myLibraryName, 
-#'         package = "stsim")
+#'              name = myLibraryName, 
+#'              package = "stsim")
 #'         
 #' # Use a default session to create a new SsimLibrary in the current working directory
 #' output <- command(args, session = session(printCmd = TRUE))

R/datasheet.R

@@ -113,9 +113,7 @@ NULL
 #' # Create a new SsimLibrary with the example template from helloworldSpatial
 #' myLibrary <- ssimLibrary(name = myLibraryName,
 #'                          session = mySession, 
-#'                          package = "helloworldSpatial",
-#'                          template = "example-library",
-#'                          forceUpdate = TRUE)
+#'                          packages = "helloworldSpatial")
 #'                          
 #' # Set the Project and Scenario
 #' myProject <- project(myLibrary, project = "Definitions")
@@ -129,28 +127,33 @@ NULL
 #' myDatasheetList <- datasheet(myScenario, summary = FALSE)
 #' 
 #' # Get a specific Datasheet
-#' myDatasheet <- datasheet(myScenario, name = "RunControl")
+#' myDatasheet <- datasheet(myScenario, name = "helloworldSpatial_RunControl")
 #' 
 #' # Include primary key when retrieving a Datasheet
-#' myDatasheet <- datasheet(myScenario, name = "RunControl", includeKey = TRUE)
+#' myDatasheet <- datasheet(myScenario, name = "helloworldSpatial_RunControl", 
+#'                          includeKey = TRUE)
 #' 
 #' # Return all columns, including optional ones
-#' myDatasheet <- datasheet(myScenario, name = "RunControl", summary = TRUE, 
-#'                          optional = TRUE)
+#' myDatasheet <- datasheet(myScenario, name = "helloworldSpatial_RunControl", 
+#'                          summary = TRUE, optional = TRUE)
 #' 
 #' # Return Datasheet as an element
-#' myDatasheet <- datasheet(myScenario, name = "RunControl", forceElements = TRUE)
+#' myDatasheet <- datasheet(myScenario, name = "helloworldSpatial_RunControl", 
+#'                          forceElements = TRUE)
 #' myDatasheet$helloworldSpatial_RunControl
 #' 
 #' # Get a Datasheet without pre-specified values
 #' myDatasheetEmpty <- datasheet(myScenario, name = "RunControl", empty = TRUE)
 #' 
 #' # If Datasheet is empty, do not return dependencies as factors
-#' myDatasheetEmpty <- datasheet(myScenario, name = "RunControl", empty = TRUE,
+#' myDatasheetEmpty <- datasheet(myScenario, 
+#'                               name = "helloworldSpatial_RunControl", 
+#'                               empty = TRUE,
 #'                               lookupsAsFactors = FALSE)
 #'                               
 #' # Optimize query
-#' myDatasheet <- datasheet(myScenario, name = "RunControl", fastQuery = TRUE)
+#' myDatasheet <- datasheet(myScenario, name = "helloworldSpatial_RunControl", 
+#'                          fastQuery = TRUE)
 #' 
 #' # Get specific SsimLibrary core Datasheet
 #' myDatasheet <- datasheet(myLibrary, name = "core_Backup")
@@ -161,7 +164,8 @@ NULL
 #'   aggregate = c("MinimumTimestep"),
 #'   where = list(MinimumTimestep = c(1))
 #' )
-#' myAggregatedDatasheet <- datasheet(myScenario, name = "RunControl",
+#' myAggregatedDatasheet <- datasheet(myScenario, 
+#'                                    name = "helloworldSpatial_RunControl",
 #'                                    sqlStatement = mySQL)
 #' }
 #' 

R/datasheetSpatRaster.R

@@ -66,10 +66,7 @@ NULL
 #' # Use the example template library from helloworldSpatial
 #' myLibrary <- ssimLibrary(name = myLibraryName,
 #'                          session = mySession,
-#'                          package = "helloworldSpatial",
-#'                          template = "example-library",
-#'                          forceUpdate = TRUE,
-#'                          overwrite=TRUE)
+#'                          packages = "helloworldSpatial")
 #' 
 #' # Set up Project and Scenario
 #' myProject <- project(myLibrary, project = "Definitions")
@@ -80,18 +77,19 @@ NULL
 #' 
 #' # Extract specific Datasheet rasters by iteration and timestep
 #' resultRaster <- datasheetSpatRaster(resultScenario,
-#'                   datasheet = "IntermediateDatasheet",
+#'                   datasheet = "helloworldSpatial_IntermediateDatasheet",
 #'                   column = "OutputRasterFile",
 #'                   iteration = 3,
 #'                   timestep = 2
 #' )
 #' 
 #' # Extract specific Datasheet SpatRasters using pattern matching
-#' resultDatasheet <- datasheet(resultScenario, name = "IntermediateDatasheet")
+#' resultDatasheet <- datasheet(resultScenario, 
+#'                              name = "helloworldSpatial_IntermediateDatasheet")
 #' colnames(resultDatasheet)
 #' outputRasterPaths <- resultDatasheet$OutputRasterFile
 #' resultRaster <- datasheetSpatRaster(resultScenario, 
-#'                   datasheet = "IntermediateDatasheet",
+#'                   datasheet = "helloworldSpatial_IntermediateDatasheet",
 #'                   column = "OutputRasterFile",
 #'                   subset = expression(grepl("ts20", 
 #'                                              outputRasterPaths,
@@ -100,10 +98,9 @@ NULL
 #' 
 #' # Return the raster Datasheets as a SpatRaster list
 #' resultRaster <- datasheetSpatRaster(resultScenario, 
-#'                  datasheet = "IntermediateDatasheet",
+#'                  datasheet = "helloworldSpatial_IntermediateDatasheet",
 #'                  column = "OutputRasterFile",
-#'                  forceElements = TRUE
-#'                  )
+#'                  forceElements = TRUE)
 #'                  
 #' # Filter for only rasters that fit specific criteria
 #' # Load the ST-Sim spatial example library
@@ -118,9 +115,7 @@ NULL
 #' # Create a new SsimLibrary with the example template from ST-Sim
 #' myLibrary <- ssimLibrary(name = myLibraryName,
 #'                          session = mySession, 
-#'                          package = "stsim",
-#'                          template = "spatial-example",
-#'                          forceUpdate = TRUE)
+#'                          packages = "stsim")
 #'                          
 #' myScenario <- scenario(myLibrary, scenario = 16)
 #' 

R/deleteLibrary.R

@@ -16,6 +16,26 @@
 #'     is FALSE.
 #' @param session Session
 #' @return "saved" or failure message.
+#' 
+#' #' @examples
+#' \donttest{
+#' # Specify file path and name of new SsimLibrary
+#' myLibraryName <- file.path(tempdir(), "testlib")
+#' 
+#' # Set up a SyncroSim Session and create SsimLibrary
+#' mySession <- session()
+#' myLibrary <- ssimLibrary(name = myLibraryName, session = mySession)
+#'  
+#' # Delete library from SsimObject
+#' deleteLibrary(myLibrary, force = TRUE, removeBackup = TRUE)
+#' 
+#' # Create another library
+#' myLibrary <- ssimLibrary(name = myLibraryName, session = mySession)
+#' 
+#' # Delete library from path
+#' deleteLibrary(myLibraryName)
+#' }
+#' 
 #' @export
 
 setGeneric("deleteLibrary", 

R/folder.R

@@ -33,7 +33,7 @@ setMethod(
 
     } else if (is.numeric(folder)){
 
-      folders <- subset(folders, Id == folder)
+      folders <- subset(folders, FolderId == folder)
 
       # If no folders retrieved, then ID does not yet exist
       if (nrow(folders) == 0){
@@ -54,8 +54,8 @@ setMethod(
 
     # If one folder retrieved, then open folder
     if ((nrow(folders) == 1) & (create == FALSE)) {
-      .Object@folderId <- folders$Id
-      .Object@parentId <- getParentFolderId(x, folders$Id)
+      .Object@folderId <- folders$FolderId
+      .Object@parentId <- getParentFolderId(x, folders$FolderId)
       .Object@session <- .session(x)
       .Object@filepath <- .filepath(x)
       .Object@projectId <- x@projectId
@@ -78,18 +78,18 @@ setMethod(
                       ". Please provide a valid parent folder name."))
         }
 
-        ParentId <- parentFolderData$Id
+        ParentId <- parentFolderData$FolderId
 
       } else if (is.numeric(parentFolder)) {
-        parentFolderData <- subset(allFolders, Id == parentFolder)
+        parentFolderData <- subset(allFolders, FolderId == parentFolder)
 
         if (nrow(parentFolderData) == 0) {
           stop(paste0("The library does not contain a folder with the ID ", 
                       parentFolder,
                       ". Please provide a valid parent folder ID"))
         }
 
-        ParentId <- parentFolderData$Id
+        ParentId <- parentFolderData$FolderId
 
       } else {
         stop("The parentFolder argument must be a character, integer, or SyncroSim folder object.")
@@ -220,15 +220,15 @@ folder <- function(ssimObject = NULL, folder = NULL, parentFolder = NULL,
         }
       }
 
-      folders <- folders[which(folders$Id %in% ids), ]
+      folders <- folders[which(folders$FolderId %in% ids), ]
     }
 
     # Subset dataframe by specified folder if summary == TRUE
     if (is(ssimObject, "Folder") & (summary == TRUE)){
-      folders <- subset(folders, Id == .folderId(ssimObject))
+      folders <- subset(folders, FolderId == .folderId(ssimObject))
     } else if (!is.null(folder) & (summary == TRUE)){
       if (is.numeric(folder)) {
-        folders <- subset(folders, Id == folder)
+        folders <- subset(folders, FolderId == folder)
       } else {
         folders <- subset(folders, Name == folder)
       }

R/folderId.R

@@ -60,7 +60,7 @@ setMethod("folderId", signature(ssimObject = "Scenario"), function(ssimObject) {
                                       item="Scenario")
   folderInfo <- getFolderData(ssimObject)
 
-  if (!parentFolderId %in% folderInfo$Id){
+  if (!parentFolderId %in% folderInfo$FolderId){
     parentFolderId <- NA
   }
 

R/name.R

@@ -22,7 +22,9 @@ NULL
 #' 
 #' # Set up a SyncroSim Session, SsimLibrary, Project, and Scenario
 #' mySession <- session()
-#' myLibrary <- ssimLibrary(name = myLibraryName, session = mySession)
+#' myLibrary <- ssimLibrary(name = myLibraryName, 
+#'                          session = mySession,
+#'                          packages = "stsim")
 #' myProject <- project(myLibrary, project = "Definitions")
 #' myScenario <- scenario(myProject, scenario = "My Scenario")
 #' myFolder <- folder(myProject, folder = "New Folder")